Role of the Tetrahemic Subunit in Desulfovibrio vulgaris

Desulfovibrio desulfuricans G20 Tetraheme Cytochrome Structure at 1.5Å and Cytochrome Interaction with Metal Complexes. M.V. Pattarkine , J.J. Tanner...
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Biochemistry 2005, 44, 14828-14834

Role of the Tetrahemic Subunit in DesulfoVibrio Vulgaris Hildenborough Formate Dehydrogenase Latifa ElAntak, Alain Dolla, Marie-Claire Durand, Pierre Bianco, and Franc¸ oise Guerlesquin* Unite´ de Bioe´ nerge´ tique et Inge´ nierie des Prote´ ines, IBSM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France ReceiVed August 2, 2005; ReVised Manuscript ReceiVed September 16, 2005

In the anaerobic sulfate-reducing bacterium DesulfoVibrio Vulgaris Hildenborough (DVH), the genome sequencing revealed the presence of three operons encoding formate dehydrogenases. fdh1 encodes an Rβγ trimeric enzyme containing 11 heme binding sites; fdh2 corresponds to an Rβγ trimeric enzyme with a tetrahemic subunit; fdh3 encodes an Rβ dimeric enzyme. In the present work, spectroscopic measurements demonstrated that the reduction of cytochrome c553 was obtained in the presence of the trimeric FDH2 and not with the dimeric FDH3, suggesting that the tetrahemic subunit (FDH2C) is essential for the interaction with this physiological electron transfer partner. To further study the role of the tetrahemic subunit, the fdh2C gene was cloned and expressed in DesulfoVibrio desulfuricans G201. The recombinant FDH2C was purified and characterized by optical and NMR spectroscopies. The heme redox potentials measured by electrochemistry were found to be identical in the whole enzyme and in the recombinant subunit, indicating a correct folding of the recombinant protein. The mapping of the interacting site by 2D heteronuclear NMR demonstrated a similar interaction of cytochrome c553 with the native enzyme and the recombinant subunit. The presence of hemes c in the γ subunit of formate dehydrogenases is specific of these anaerobic sulfate-reducing bacteria and replaces heme b subunit generally found in the enzymes involved in anaerobic metabolisms. ABSTRACT:

In prokaryotes the formate, produced from pyruvate during anaerobic respiration, serves as the major electron donor to a variety of respiratory pathways that use terminal acceptors other than oxygen. Formate dehydrogenases (FDHs)1 are metalloenzymes which catalyze the oxidation of formate to CO2 and H+. These enzymes contain either Mo or W associated to molybdopterin guanidine dinucleotide (MGD) cofactors and a conserved selenocysteine (SeCys) residue at their active site. Formate dehydrogenases isolated from anaerobic organisms are structurally related, but their contents in subunits and prosthetic groups are highly diversified. The structures of three bacterial enzymes have been solved by X-ray: FDH-H and FDH-N from Escherichia coli (1, 2) and FDH from DesulfoVibrio gigas (3). FDH-H is the constitutive formate dehydrogenase of E. coli which is part of the anaerobic formate hydrogen-lyase complex. This monomeric enzyme is organized in four main domains and contains a selenocysteine (SeCys), a molybdenum atom coordinated by two molybdopterin guanine dinucleotide (MGD) cofactors, and an iron-sulfur cluster at the active site (1). The FDH-N from E. coli is a nitrate-inducible enzyme expressed in anaerobic conditions. This molybdoenzyme contains three subunits: the catalytic R subunit coordinates a bis-MGD cofactor and one iron-sulfur (FeS) cluster, the β subunit holds four (FeS) clusters, and the membrane-bound γ subunit * Corresponding author. E-mail: [email protected]. Tel: 33 (0) 491 164 379. Fax: 33 (0) 491 164 578. 1 Abbreviations: NMR, nuclear magnetic resonance; FDH, formate dehydrogenase; DVH, DesulfoVibrio Vulgaris Hildenborough; HSQC, heteronuclear single-quantum correlation.

incorporates two b-type hemes (2). D. gigas FDH (DgWFDH) is a tungsten-containing enzyme composed of two subunits: the R subunit, which includes the W binding site and one (FeS) cluster, and the β subunit, which contains three (FeS) clusters. Trimeric periplasmic formate dehydrogenases have been isolated from both DesulfoVibrio Vulgaris Hildenborough (4) and DesulfoVibrio desulfuricans ATCC7757 (5). These enzymes include, in addition to the R and β subunits, a γ subunit which holds four c-type hemes. The genome of D. Vulgaris Hildenborough (DVH) has been recently sequenced and reveals the presence of three operons encoding different formate dehydrogenases (6). The fdh1 operon contains three genes encoding an Rβγ trimer. The γ subunit (FDH1C) includes 11 heme c binding sites. The fdh2 operon corresponds to the well-characterized enzyme (4), which contains a tetrahemic subunit (FDH2C) homologous to the soluble tetrahemic cytochromes found in all the DesulfoVibrio species (7). The third operon, fdh3, encodes an Rβ dimer, homologous to DgW-FDH subunits. We have in previous work isolated the three enzymes and analyzed their expression in D. Vulgaris Hildenborough (4, 8). Cytochromes c3 are low oxidoreduction potential multihemic cytochromes only found associated to the anaerobic metabolism of DesulfoVibrio and Shewanella. This class of cytochromes is characterized by the presence of four bishistidinyl axial coordinated hemes. The structures of cytochromes c3 from various DesulfoVibrio species have been solved by X-ray, and despite the low sequence identity, their three-dimensional structures are highly conserved, containing

10.1021/bi0515366 CCC: $30.25 © 2005 American Chemical Society Published on Web 10/21/2005

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Table 1: Strains and Plasmids for fdh2C Gene Expression strain or plasmid E. coli TG1 D. Vulgaris Hildenborough NCIMB 8303 D. desulfuricans G201 pJ800 pBMK7 p800fdh2C pK800fdh2C

genotype, comment, and/or ref E. coli K12 ∆(lac-pro)supE thi hsdD5 (F′traD36proA+B+ lacIq lacZDM15) isolated from clay soil near Hildenborough, U.K. (24) spontaneous Nalr derivative of D. desulfuricans G100A contains cyc gene of D. Vulgaris Hildenborough on a 640-bp EcoRI-HindIII insert in pUC8 (25) broad-host range vector; Kmr (26) pJ800 containing the cyc-fdh2C gene fusion (this study) contains the cyc-fdh2C gene fusion on a 694-bp EcoRI-HindIII fragment insert in pBMK7 (this study)

a typical heme core arrangement (7). The DVH genome contains numerous genes encoding multihemic c-type cytochromes (6). In the present work, we have shown that the tetrahemic subunit (FDH2C) is necessary to reduce cytochrome c553, the physiological redox partner of DVH formate dehydrogenase (4). We have cloned and expressed the FDH2C subunit and investigated, by heteronuclear NMR, its role in the complex formation with DVH cytochrome c553. MATERIALS AND METHODS Strains, Vectors, and Media. The bacterial strains and plasmids used in this study are described in Table 1. Growth of E. coli was carried out using tryptone-yeast extract medium at 37 °C supplemented with the appropriate antibiotic (0.27 mM ampicillin or 0.17 mM kanamycin) when needed. D. Vulgaris Hildenborough as well as wild-type and recombinant D. desulfuricans G201 strains was cultured in medium C (9) at 32 °C in an anaerobic COY chamber (10% CO2, 5% H2, 85% N2) supplemented with kanamycin (0.28 mM) when required. Cloning and Expression of the fdh2C Gene. Two phosphorylated primers, CYC32ATG (5′P-AGATACCTGGTCATCTCCCT3′) and CYC32STOP (5′P-CTATTTCTTCTCGGACGCC3′), were designed in order to PCR-amplify, from D. Vulgaris Hildenborough genomic DNA, the gene encoding FDH2C (DVU2809) (6). The resulting 432-bp DNA fragment was named fdh2C. Circular plasmid pJ800 containing the cyc gene (Table 1) was amplified by PCR with primers C3ATG (5′CATGATCGAACTACCTCC3′) and C3STOP (5′GCAGTACAGACTGACGCA3′) using the Expand high-fidelity PCR system (Roche). The resulting 2.89-kb fragment was gel-purified and ligated with the 432bp fdh2C fragment to give p800fdh2C. The sequence of the resulting cyc-fdh2C gene fusion was verified by DNA sequencing. Plasmid p800fdh2C was digested with both EcoRI and HindIII, and the resulting 694-bp fragment was subcloned into pBMK7 digested with the same two enzymes. The resulting plasmid (pK800fdh2C) was used for electrotransformation of D. desulfuricans G201 as previously described (10). The recombinant D. desulfuricans G201 (pK800fdh2C) strain was selected using kanamycin. Protein Purification. The cytochrome FDH2C was purified from recombinant D. desulfuricans G201 (pK800fdh2C) cultured in 300 L of medium C (9) supplemented with 0.28 mM kanamycin. Cells (300 g wet weight) were incubated

FIGURE 1: Time course of the reduction of cytochrome c553 by FDH2 and FDH3 from DVH. The experiments were carried out at 25 °C following the variation of the absorption at 553 nm. The cytochrome c553 and FDH concentrations were 10 µM and 1 nM, respectively.

for 30 min at 37 °C in 0.1 M Tris-HCl and 0.1 M EDTA (pH 9.0). After centrifugation (10000g, 1 h, 4 °C), the supernatant which contains the periplasmic proteins was dialyzed against 10 mM Tris-HCl buffer (pH 7.6). The periplasmic extract was then loaded onto a DEAE-52 column equilibrated with 10 mM Tris-HCl buffer (pH 7.6) and eluted using a step gradient. The FDH2C cytochrome subunit was eluted with 50 mM Tris-HCl buffer (pH 7.6) whereas the cytochrome c3 from D. desulfuricans G201 was eluted with 100 mM Tris-HCl buffer (pH 7.6) as previously reported (11). The FDH2C-containing fraction was then loaded onto a hydroxyapatite column. The FDH2C subunit was eluted in 140 mM phosphate buffer. Purity of the protein was checked by electrophoresis on polyacrylamide gel under denaturing conditions. The purity index, defined as (Ared553 - Ared570)/Aox280, was 1.7. FDH2 and FDH3 were isolated from the DVH extract using a step gradient of Tris-HCl buffer (pH 7.6) performed on a DEAE-52 column; FDH2 was eluted with 100 mM buffer and FDH3 with 400 mM buffer (4, 8). Uniformly 15Nlabeled cytochrome c553 was expressed and purified from DdG201(pRC41) as previously described (12). ActiVity Assays. The time course of cytochrome c553 reduction by formate dehydrogenase was carried out at 25 °C on a ThermoSpectronic spectrophotometer, using absorption at 553 nm. The reaction mixture contained 10 mM glycine/NaOH buffer at pH 8.3 and 20 mM formate. The cytochrome and formate dehydrogenase concentrations were respectively 10 µM and 1 nM. Characterization of the FDH2C Subunit. (A) Protein Sequencing. The N-terminal of the FDH2C sequence was performed by stepwise Edman degradation using an automatic Procise 494 sequanator. (B) Redox Potential Measurements. Cyclic voltammetry (CV) experiments were carried out using an EG&G 273A potentiostat modulated by EG&G PAR M270/250 software. A three-electrode cell consisting of a Metrohm (M/m) Ag/ AgCl/saturated NaCl reference electrode (at 210 mV vs normal hydrogen electrode), a gold wire auxiliary electrode, and a working pyrolytic graphite electrode was used. All experiments were done at room temperature in 10 mM potassium phosphate buffer (pH 5.9).

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FIGURE 2: (A) UV-visible spectra of FDH2C. The oxidized form corresponds to the continuous line, and the reduced form corresponds to the dotted line. Reduction was obtained by addition of sodium dithionite. (B) 1D NMR spectrum of the FDH2C subunit at 0.4 mM concentration. (C) Cyclic voltammograms at the pyrolytic graphite electrode of the FDH2C subunit (30 µM) in 10 mM potassium phosphate buffer, pH 5.9. The dotted line corresponds to the buffer solution alone. The scan rate was 20 mV‚s-1.

(C) Optical Spectrum. Absorption spectra from 260 to 600 nm were recorded on a ThermoSpectronic spectrophotometer. NMR Experiments. NMR experiments were recorded at 296 K on a Bruker Avance DRX 500 spectrometer. NMR samples were prepared in 10 mM potassium phosphate buffer (pH 7.6) and 10% D2O. 2D NMR spectra (15N-1H HSQC) were performed on 15N-labeled cytochrome c553 at 14 µM concentration. The cytochrome was reduced with 2 equivalents of sodium dithionite. In the presence of an equimolar amount of FDH2, cytochrome c553 was reduced by adding sodium formate (50 mM). The spectral widths were 2500

Hz for 1H and 2027 Hz for 15N. A total of 1024 data points were used in t2, and 64 transients were recorded for each 128 t1. RESULTS Role of FDH2C in the Reduction of the Physiological Partner: Cytochrome c553. In the periplasm of D. Vulgaris Hildenborough, the FDH enzyme oxidizes formate and transfers the resulting electrons to the monohemic cytochrome c553 (4, 13). FDH2 and FDH3 are very similar, sharing 53% and 56% identities between their R and β

Tetrahemic Subunit in FDH

FIGURE 3: Cytochrome c553/FDH2 complex formation. (A) Superimposition of HSQC spectra of ferrocytochrome c553 (in black) and ferrocytochrome c553 in the presence of 1:1 FDH2 after reduction by formate in anaerobic conditions (in red). Black boxes contain cross-peaks that disappear upon complex formation (residue numbering). Red boxes contain cross-peaks that undergo chemical shift variations during complex formation. (B) Chemical shift variations observed from panel A. The relative variations of 1H and 15N were calculated according to ref 27. Stars indicate the residues which disappear during the complex formation.

subunits, respectively. However, FDH3 is depleted of the γ subunit. We have tested the reduction of cytochrome c553 by FDH3 (Figure 1). No reduction of the monohemic cytochrome c553 was observed. In contrast, the cytochrome c553 reduction was observed in the presence of FDH2. These data suggest that FDH2C, the γ subunit of the formate dehydrogenase, is essential for a productive electron transfer to its physiological partner, the cytochrome c553. To further study the role of the FDH2C subunit, we have produced the recombinant protein in D. desulfuricans G201 and investigated its interaction with cytochrome c553 using heteronuclear NMR. FDH2C Production and Purification. The fdh2 operon is composed of three genes encoding respectively the R, β, and γ subunits of the already characterized DVH formate dehydrogenase (4). The γ subunit (FDH2C) encoded by the third gene (DVU2809) is expected to be a c-type heme-containing molecule. To produce this single subunit, which is named hereafter FDH2C, the coding region was inserted into an expression vector based on the cyc transcription unit from D. Vulgaris Hildenborough (14). The construction was designed so that the coding region of the cyc gene was replaced by that of the fdh2C gene. The use of the cyc transcription unit has been already shown to be highly effective for the heterologous production of multiheme cytochromes in D. desulfuricans G201 (10).

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FIGURE 4: Cytochrome c553/FDH2C complex formation. (A) Superimposition of HSQC spectra of ferrocytochrome c553 (in black) and ferrocytochrome c553 in the presence of 1:1 FDH2C subunit after reduction by sodium diothinite (in red). Black boxes contain cross-peaks that disappear upon complex formation (residue numbering). Red boxes contain cross-peaks that undergo chemical shift variations during complex formation. (B) Chemical shift variations observed from panel A. The relative variations of 1H and 15N were calculated according to ref 27. Stars indicate the residues which disappear during the complex formation.

The purification procedure described in Materials and Methods allowed us to get 3.14 mg of pure FDH2C subunit from 300 L of culture. Only one band was detected on the gels, corresponding to a relative molecular mass of 15 kDa. It is to be noted that while the heterologous production of the tetraheme cytochrome c3 (Mr 13000) from DVH in D. desulfuricans G201 was very efficient (11), the production of the FDH2C subunit is much lower. FDH2C is a part of a multimeric enzyme and may be less stable when it is produced as recombinant single protein. Characterization of the Recombinant FDH2C Subunit. The NH2-terminal sequence of the recombinant FDH2C subunit was found to be ADAAKA. According to the translated gene sequence of DVU2809 (6), the signal sequence is correctly cleaved in D. desulfuricans G201. The UV-visible spectrum of the FDH2C subunit presents different absorption bands, characteristics of c-type heme-containing proteins (Figure 2A). The oxidized state of the protein shows two absorption maxima at 409 nm (Soret) and 530 nm. Upon reduction by sodium dithionite, the Soret band intensifies and shifts to 418 nm, while the R and β bands appear at 552 and 523 nm, respectively. It should be noticed that the same absorp-

14832 Biochemistry, Vol. 44, No. 45, 2005 tion bands were found in the UV-visible spectrum of native FDH2 (4), indicating that the hemes are correctly inserted in the recombinant subunit. Moreover, in the low-field part of the 1D NMR spectrum of the FDH2C subunit, wellresolved resonances are assigned to the 16 heme methyl lines (Figure 2B). Finally, the shape of the forward and backward traces of cyclic voltammetry curves (Figure 2C) indicates a reversible electrochemical process corresponding to the reduction-reoxidation of the hemic centers. The plots for the native FDH2 and the FDH2C subunit are similar, because iron-sulfur clusters are not electroactive in these conditions as observed for other (FeS) enzymes such as hydrogenases (15). The deduced macroscopic oxidoreduction potentials of the four hemes are centered at -220 mV. The values obtained for the recombinant tetrahemic subunit and the native enzyme were quite similar, with a small shift toward lower potential values for the recombinant cytochrome. These data indicate that the R and β subunits do not have any drastic effect on the modulation of the heme redox potentials of the FDH2C subunit. NMR Mapping of FDH2 and FDH2C Interacting Sites. 1 H-15N HSQC experiments correspond to the fingerprint of the protein where each cross-peak represents the amide group of an amino acid. Complex formation induces 15N or/and 1 H chemical shifts of the residues located at the interacting interface. In the NMR spectrum of DVH cytochrome c553 already assigned (12), nine resonances are affected by the presence of FDH2 (Figure 3). Five resonances (G3, G33, S65, D66, and E67) shift from their position in the free protein to a position corresponding to the bound form, indicating a fast exchange between the two states, at the NMR time scale. The line width of all the resonances increases notably with the size of the binary complex, but due to the fast exchange most of the resonances are still observable. However, four resonances (A21, M23, E52, and K63) shifting at low concentrations disappear with increasing concentrations of FDH2. In the presence of the FDH2C subunit, only eight resonances are affected by the complex formation (Figure 4). The resonances of residues G3, A21, G33, K63, and S65 shift, and three resonances (M23, E52, and M57) disappear upon complex formation. Comparison of the interacting sites (Figure 5) reveals that ∼80% of the affected residues on cytochrome c553 are common to both complexes. This result indicates that the tetrahemic subunit of FDH2 is the cytochrome c553 interacting site and thus corresponds to the electron gate of the FDH2 enzyme.

ElAntak et al.

FIGURE 5: Mapping of the FDH2 interacting site (top) and the FDH2C subunit interacting site (bottom) on DVH cytochrome c553. The heme surface is colored in red, and affected residues in the NMR spectra are shown in green.

DISCUSSION The genome sequence of D. Vulgaris Hildenborough shows the presence of three gene clusters encoding formate dehydrogenases (6). Two of these enzymes contain a multihemic subunit. Multimeric formate dehydrogenases are common in bacteria; some of them, like FDH-N from E. coli (2), contain membrane-bound b-type cytochromes which transfer electrons to quinones. However, the presence of low redox potential c-type hemes in formate dehydrogenases is specific to sulfate-reducing bacteria. In the present work, we have established that this hemic subunit, FDH2C, is required to reduce the physiological partner, cytochrome c553. To understand the role of this tetrahemic subunit in DVH formate dehydrogenase, we have produced the FDH2C subunit in D. desulfuricans G201. Using 2D NMR mapping on cyto-

FIGURE 6: Mapping of the [Fe]-hydrogenase interacting site (top) and the ferredoxin interacting site (bottom) on DVH cytochrome c553 from refs 18 and 19. The heme surface is colored in red, and affected residues in the NMR spectra are shown in green.

chrome c553, we have demonstrated that the interacting sites of the native FDH2 and the recombinant FDH2C are similar (Figure 5) and conclude that FDH2C is the electron gate of the enzyme. The presence of two additional cytochrome c553 acidic residues (D66 and E67) in the complex with FDH2 (Figure 5) is probably due to the necessity of a larger

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FIGURE 7: Sequence alignment of D. Vulgaris Hildenborough cytochromes c3: FDH2C, multihemic subunit of DVH FDH2 formate dehydrogenase; c3I-DvH, type I cytochrome c3; c3II-DvH, type II cytochrome c3. Heme binding sites are in black boxes, lysine residues conserved in the type I cytochrome c3 family are colored in blue, and acidic residues conserved in the type II cytochrome c3 family are colored in red.

interacting surface with the whole enzyme (124.5 kDa) compared to the recombinant subunit (15 kDa). One can expect that at least one of the two other subunits of the native formate dehydrogenase is involved in the molecular interface. It has been previously shown by enzymatic analysis that replacement of the K63 residue by a glutamate residue had a drastic effect on the FDH2/cytochrome c553 complex formation (16). K63 is perturbed in the 2D NMR spectra for both complexes (Figures 3 and 4). This result confirms that K63 is at the interacting surface of the two complexes and plays an important role for the FDH2/cytochrome c553 complex formation. Y64 has also been shown to be essential for the electron transfer between FDH2 and cytochrome c553 (17). The role of this aromatic residue is not yet well understood, but in all of the structural models of electron transfer complexes involving cytochrome c553, Y64 is found at the electron transfer site (18, 19). It is to be noticed that the Y64 NH group is not affected by the presence of FDH2 and FDH2C. However, the resonances of the neighbor residues are very much altered, which is consistent with an involvement of Y64 in the electron transfer process in these two complexes. Figure 6 represents the cytochrome c553 interacting surfaces for complexes involving ferredoxin and [Fe]-hydrogenase (18, 19). Most of the residues involved in these complexes are found in the FDH2 complex. However, three additional residues (S65, D66, and E67) are only found at the interface of the complex with FDH2 (Figure 5), which reveals the differences of surface complementarities between cytochrome c553 and its physiological partners. The cytochrome c3 family is a large class of multihemic soluble cytochromes. Two types of tetrahemic cytochromes c3 have been characterized, namely, type I and type II cytochromes c3. Type I cytochrome c3 acts as an electron shuttle in the periplasm between the cytochrome Hmc and the [Fe]-hydrogenase (20, 21). In these two electron transfer complexes, heme 4 of cytochrome c3 is the reactive heme bordered by conserved lysine residues. Type II cytochromes c3 are acidic soluble cytochromes associated to membranebound electron transfer complexes (22). The three-dimensional structure of the type II cytochrome c3 from DesulfoVibrio africanus shows that conserved acidic residues are found around the putative reactive heme 1 (23). The tetrahemic subunit of FDH2 contains some of the conserved lysine residues found in the type I cytochromes c3 and some of the conserved acidic residues characteristic of the type II cytochromes c3 (Figure 7). Thus, the FDH2C subunit does not belong to any of these two families, and one can propose

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